Welcome to the NuGO R-server!

Page contents:

On this page, you can find R/Bioconductor libraries for Unix/Linux and
Windows specific for R-2.10.x:
1. Bioconductor support libraries for the human and mouse NuGO arrays.
2. Bioconductor annotation libraries for the Affymetrix Gene Titan
system.
3. Bioconductor libraries for the MBNI
Custom Chip Definition Files (CDFs) for the human and mouse NuGO
arrays (cdf, probe, and Entrez gene annotation).
4. For the current MBNI
Custom Chip Definition Files (CDFs) release: Bioconductor libraries for
human,
mouse, and rat species that we support (Entrez gene; also probe and cdf)*.
5. For the previous MBNI
Custom Chip Definition Files (CDFs) release: Bioconductor libraries for
human,
mouse, and rat species that we support (Entrez gene; also probe and cdf)*.

*: For
convenience, we mirror the probe and CDF files as provided by MBNI.
The annotation libraries are created by ourselves. We provide only the
Entrezg libraries, and tairg for Arabidopsis.

REMARK:
we decided to use the ENTREZ Custom CDF-files for the following reasons:

Most up-to-date.

Corresponds to genes (not transcripts).

Accepted input for follow-up analyses.

Off course, you are free to use one of the other formats, e.g. ENSEMBL,
but we do not provide Bioconductor annotation libraries for those
custom CDFs.

Custom CDFs:Please do this if you receive an error message on missing
libraries (only the lacking libraries need to be installed):
source("http://www.bioconductor.org/biocLite.R")
biocLite(c("org.At.tair.db", "org.Hs.eg.db",
"org.Mm.eg.db", "org.Rn.eg.db"))

Current Custom CDf is version 12.0.0 (27 October 2009). Previous Custom
CDF is version
11.0.1 (12 November 2008).
If new Custom CDF libraries are released, the versions will shift up
(and the current "previous" repository will be dropped).
Please check the tables below to see whether your chip is supported!
Simply use the proper library names in the commands as shown in the
examples above.

Manual Installation

Installation instructions

For Windows: download the appropriate .zip-files from the tables below.
In RGui, go to Packages => Install package(s) from local
zip-files...
Browse to the location where you downloaded your .zip-files and select
the files you want to install. Done!

For Unix/Linux: download the appropriate .tar.gz files from the tables
below. cd to the directory where you downloaded your .tar.gz files and
execute the following command (multiple times for multiple .tar.gz
files): R CMD INSTALL <your downloaded.tar.gz file>.

Download tables

1. Human and mouse NuGO array support files as provided on the
Bioconductor web site (27 October 2009).
Here, also the CDF and PROBE libraries are available
for download. To
obtain full microarray support, you need to download and install all
three libraries for each species!

2. Human and mouse NuGO array support files (VERSION 12.0.0;
MBNI
Custom CDF; 27 October 2009).
Here, also the CDF and PROBE libraries are available
for download. To
obtain full microarray support, you need to download and install all
three libraries for each species!

3. Annotation libraries for the MBNI
Custom CDF annotation files (VERSION 12.0.0;
updated 27 October 2009). Here, also
the CDF and PROBE libraries are available for download. To
obtain full microarray support, you need to download and install all
three libraries for each species!

4. Human and mouse NuGO array support files (VERSION 11.0.1;
MBNI
Custom CDF; 28 October 2009).
Here, also the CDF and PROBE libraries are available
for download. To
obtain full microarray support, you need to download and install all
three libraries for each species!

5. Annotation libraries for the MBNI
Custom CDF annotation files (VERSION 11.0.1;
updated 28 October 2009). Here, also
the CDF and PROBE libraries are available for download. To
obtain full microarray support, you need to download and install all
three libraries for each species!